Using the QT4D Plugins Page 1 Using Hardin Lab QuickTime and ...

Using the QT4D Plugins Page 1
Using Hardin Lab QuickTime and 4d Plugins – Fall, 2007
Jeff Hardin – Department of Zoology, University of Wisconsin-Madison
jdhardin@wisc.edu
1) Accessing the plugins:
The plugins can be accessed in one of two basic ways:
(a) Through the ImageJ plugins menu:
Figure 1 – Selecting QuickTime plugins using the ImageJ Plugins menu
If the plugins are installed manually, they can be accessed via the "Plugins" menu in
ImageJ [note: most screen shots show ImageJ running under Mac OS X, but the interface
is essentially identical under Windows, and, with limitations, under Mac OS 9].
(b) Through the 4d toolset:
QT4D
Player
tool
QT4D
Writer
tool
Browse
4D tool
QuickTime
movie tools
Figure 2 – Selecting QuickTime plugins using the ImageJ Plugins menu
3d rotation
tools
Select
toolsets
here
Installing the "4d Tools.txt" toolset in the macros->toolsets directory within the main
ImageJ directory allows access to a toolset that can be selected using the >> button at the
right of the ImageJ main window. Selecting "4d Tools" loads the buttons shown in Figure
2. Note: this feature requires ImageJ 1.37t or later.
(2) QT4D Player
(a) Opening movies: When the plugin is invoked, you will be asked to open a movie. The plugins
looks for a simple text file that contains information about the movie that has the same root name

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as the movie itself (e.g., if the movie is called "foo.mov", then it will look for a file called
"foo.mov.info" or "foo.mov.txt"). If it cannot find one, then it will ask you for the number of
focal planes in the movie.
Advanced tip: The data structure of the info file is very simple. It is a text file with the following lines,
separated by carriage returns:
Line 1: A text string with basic information about the movie
Line 2: The number of focal planes in the movie as an integer
Line 3: The spacing (assumed to be in microns) between focal planes
Line 4: The time interval between acquisition of Z series
Line 5: Blank [this deals with a quirk in the way Java under Mac OS 9 handled text files]
You can easily recreate an info file using your favorite vanilla text editor using this basic
structure.
(b) Navigating through a movie: You can navigate through movies in several ways:
(i) Arrow keys: The arrows keys on the keyboard can be used to navigate up and down and
backwards and forwards through a movie. Frames in the movie will be skipped based on the
information in the associated info file, or based on the number of focal planes you entered when
asked.
Figure 3 – The main QT4D Player window
Edges allow
navigation
Use the
slider to
navigate
through time
Hold down
buttons to move
through space
or time

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ii) Buttons: Holding down the mouse on the stepper buttons (except under Mac OS 9)
allows repeated steps forward, back, up, or down.
(iii) Mouse-based 4d navigation: At the edges of the movie window, the cursor will
change to a forward/back symbol or up/symbol. In these regions of the movie, holding
down the mouse will likewise step in the appropriate directions (left edge = back; right
edge = forward; top edge = up; bottom edge = down).
Figure 4 – Contextual menu options
(c) Other features of the main QT4D
player window: There are several
convenient – but non-obvious –
features in the main movie player
window. Right-clicking
(Windows)/Clicking with the Control
key pressed (Mac OS X): In addition,
control-clicking (or right clicking) on
the movie window brings up several
options, including copying the data to
standard ImageJ objects in various
ways, getting information about the
movie sequences from its info file, etc. If the movie has been zoomed, the "Reset
Window to Original Size" command allows reversion to the original movie/window
dimensions.
(i) "Get info…": When this option ius selected, information about the movie will be
displayed:
Figure 5 – The movie information window
(ii) Show/Hide Controls: When this option is selected, the visibility of the buttons at the
bottom of the movie window will be toggled.

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(iii) Apply Filter… : Experimental support is provided for applying temporary filters to a
movie. This can be useful for applying brightness/contrast changes, sharpening filters,
etc. This feature uses QuickTime filtering to add a temporary, non-destructive filter to a
movie.
Figure 6 – Selecting the "Apply filter" option
When this option is selected, a list of filters provided by QuickTime will appear:
Figure 7 – Selecting a QuickTime filter

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The contextual menu contains a "Revert to original…" option to remove the filter.
(4) QT4D Writer: This plugin is used to convert folders of single images arranged as
captured in a 4d dataset into a QuickTime movie.
Running the plugin causes a file dialog to appear asking for the location of the raw files.
Select the folder, and then one of the images:
Figure 8 – Specifying a directory with images for QT4D Writer
Next, if there is no information file, you will be asked to supply information regarding
the number of focal planes (important; 33 in this case) and other information in a series of
dialogs:
Figure 9 – Specifying the number of focal planes
Next, you will be presented with a standard compression dialog box [Note: due to a bug
under OS X/1.4.1+ VM, the frame rate options and key frames will be in a separate
dialog. Under other operating systems, they will appear as shown]:

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Figure 10 – Selecting compression parameters for the movie
Finally, you will be asked where to save the movie. After clicking "OK" to proceed, a
progress indicator will appear during compression, which also allows cancellation of the
compression:
Figure 11 – The progress dialog during compression
(4) Browse4D: This plugin is used for browsing through a folder of single images that
comprise a 4d dataset. The window behaves like a standard ImageJ image window in
terms of edit commands, etc., but has an interface that is essentially identical to that of
the QT4D Player plugin. It has an advantage over other plugins, such as the Image5D
plugin, in that it does not load image data into RAM. This makes it less intensive in terms
of computing resources, but slower for moving rap[idly through a large number of large
images.

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Figure 12 –The Browse4D window
Step back Step forward Step up Step down
First time pt Play
Last time pt
(5) Acquire 4D: This plugin is used in the Hardin Lab to acquire Nomarski 4D datasets
using video cameras and Scion AG-5 framegrabbers. Although this digitization
technology is old, the rest of the code could serves as a basis for using more modern
Firewire cameras for data acquisition.
Invoking the plugin brings up a dialog in which parameters for the movie are entered:
Figure 13 – Specifying parameters for a 4d movie

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The "use shutter" option allows use of a shutter during acquisition. The root name for
files is the basic name for files, to which numbers are appended. If the root name is "foo",
files will be named "foo0001.tif", "foo0002.tif", etc.
Once parameters are entered, a confirmation dialog will appear:
Figure 14 –Reviewing parameters
If you click "OK", an ImageJ window will open, the shutter will open (if this option was
selected), and a standard "Save As…" dialog will appear asking where you wish to save
the image files for the movie. Once you specify where files will be saved, the first Z
series will be acquired, the shutter will close, and the standard control window will
appear:
Figure 15 – The main 4D Capture windows

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The "Stop capture" button does what is says. Live preview and cessation of live previewing are
accomplished using the "Live preview" and "Stop preview" buttons. Clicking the "Live preview"
button bring up a modified Scion live preview window:
Figure 16 –The Live Preview window
Clicking the "Stop preview" button will stop the preview and hid the Preview window.
Clicking its close box hides the window as well. A few seconds before a Z-series is
acquired, if a Live Preview window is open, acquisition will stop to give processor time
to the Z series being acquired. Once the Z series is acquired, live previewing resumes.
The "Down" and "Up" buttons will adjust the focal plane during acquisition.
Once a 4d dataset has been acquired, it can be viewed as raw images using the Browse4D
plugin, compiled using the QT4D Writer plugin, and viewed using the QT4D Player
plugin.
Good luck and happy 4d navigating!